{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pinecone-io/examples/blob/master/integrations/haystack/nhs-search/notebooks/00_indexing.ipynb) [![Open nbviewer](https://raw.githubusercontent.com/pinecone-io/examples/master/assets/nbviewer-shield.svg)](https://nbviewer.org/github/pinecone-io/examples/blob/master/integrations/haystack/nhs-search/notebooks/00_indexing.ipynb)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Indexing Data\n",
    "\n",
    "Before we can perform question-answering (QA) operations we much initialize a document store which will store all of our source text and allow us to ask questions in reference to this source text. The process of initializing the document store and adding data to it is called *indexing*.\n",
    "\n",
    "## Load Data\n",
    "\n",
    "Before we begin indexing we must load and prepare our dataset. We are using an NHS dataset from Deepset, these same files can be downloaded from the demo repository. TK link\n",
    "\n",
    "We load them from the `/data` directory like so:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['../data/www.nhs.uk_conditions_pre-eclampsia_.txt',\n",
       " '../data/www.nhs.uk_conditions_acute-lymphoblastic-leukaemia_.txt',\n",
       " '../data/www.nhs.uk_conditions_homeopathy_.txt',\n",
       " '../data/www.nhs.uk_conditions_blushing_.txt',\n",
       " '../data/www.nhs.uk_conditions_ehlers-danlos-syndromes_.txt']"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from pathlib import Path\n",
    "\n",
    "paths = [str(x) for x in Path('../data').glob('*.txt')]\n",
    "paths[:5]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "These are all plaintext files that contain NHS information on a particular condition like *pre-exlampsia*, *acute-lymphoblastic-leukaemia*, etc. Let's see how many of these files we have..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "953"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(paths)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We will load them all into a variabled called `nhs_text`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "nhs_text = []\n",
    "for path in paths:\n",
    "    with open(path, 'r') as fp:\n",
    "        text = fp.read()\n",
    "        nhs_text.append(text)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's see what they look like:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Cookies on the NHS website\\nWe\\'ve put some small files called cookies on your device to make our site work.\\nWe\\'d also like to use analytics cookies. These send information about how our site is used to services called Adobe Analytics, Hotjar and Google Analytics. We use this information to improve our site.\\nLet us know if this is OK. We\\'ll use a cookie to save your choice. You can read more about our cookies before you choose.\\nI\\'m OK with analytics cookies Do not use analytics cookies\\nSearch the NHS website\\nSearch\\nMy account\\nHealth A-Z\\nLive Well\\nMental health\\nCare and support\\nPregnancy\\nBrowse\\nMore\\nHome Health A to Z\\nOverview\\n-\\nPre-eclampsia\\nContents\\nOverview\\nSymptoms\\nCauses\\nDiagnosis\\nTreatment\\nComplications\\nPre-eclampsia is a condition that affects some pregnant women, usually during the second half of pregnancy (from 20 weeks) or soon after their baby is delivered.\\nImportant:\\nCoronavirus (COVID-19) update\\nIf you\\'re well, it\\'s really important you go to all your appointments and scans for the health of you and your baby.\\nIf you\\'re pregnant, hospitals and clinics are making sure it\\'s safe for you to go to appointments.\\nIf you get symptoms of COVID-19, or you\\'re unwell with something other than COVID-19, speak to your midwife or maternity team. They will advise you what to do.\\nFind out more about pregnancy and COVID-19\\nSymptoms of pre-eclampsia\\nEarly signs of pre-eclampsia include having high blood pressure (hypertension) and protein in your urine (proteinuria). \\nIt\\'s unlikely that you\\'ll notice these signs, but they should be picked up during your routine antenatal appointments.\\nIn some cases, further symptoms can develop, including:\\nsevere headache\\nvision problems, such as blurring or flashing\\npain just below the ribs\\nvomiting\\nsudden swelling of the face, hands or feet\\nIf you notice any symptoms of pre-eclampsia, seek medical advice immediately by calling your midwife, GP surgery or NHS 111.\\nAlthough many cases are mild, the condition can lead to serious complications for both mother and baby if it\\'s not monitored and treated. \\nThe earlier pre-eclampsia is diagnosed and monitored, the better the outlook for mother and baby.\\nVideo: what is pre-eclampsia and what are the warning signs?\\nIn this video, a midwife explains the warning signs of pre-eclampsia.\\nPlay Video\\nMedia last reviewed: 1 September 2020\\nMedia review due: 1 September 2023\\nWho\\'s affected?\\nThere are a number of things that can increase your chances of developing pre-eclampsia, such as:\\nhaving diabetes, high blood pressure or kidney disease before you were pregnant\\nhaving an autoimmune condition, such as lupus or antiphospholipid syndrome\\nhaving high blood pressure or pre-eclampsia in a previous pregnancy\\nOther things that can slightly increase your chances of developing pre-eclampsia include:\\na family history of pre-eclampsia\\nbeing 40 years old or more\\nit\\'s more than 10 years since your last pregnancy\\nexpecting multiple babies (twins or triplets)\\nhaving a body mass index (BMI) of 35 or more\\nIf you have 2 or more of these together, your chances are higher.\\nIf you\\'re thought to be at a high risk of developing pre-eclampsia, you may be advised to take a 75 to 150mg daily dose of aspirin from the 12th week of pregnancy until your baby is born.\\nWhat causes pre-eclampsia?\\nAlthough the exact cause of pre-eclampsia is not known, it\\'s thought to occur when there\\'s a problem with the placenta, the organ that links the baby\\'s blood supply to the mother\\'s.\\nTreating pre-eclampsia\\nIf you\\'re diagnosed with pre-eclampsia, you should be referred for an assessment by a specialist, usually in hospital.\\nWhile in hospital, you\\'ll be monitored closely to determine how severe the condition is and whether a hospital stay is needed.\\nThe only way to cure pre-eclampsia is to deliver the baby, so you\\'ll usually be monitored regularly until it\\'s possible for your baby to be delivered.\\nThis will normally be at around 37 to 38 weeks of pregnancy, but it may be earlier in more severe cases.\\nAt this point, labour may be started artificially (induced) or you may have a caesarean section.\\nYou\\'ll be offered medicine to lower your blood pressure while you wait for your baby to be delivered.\\nComplications\\nAlthough most cases of pre-eclampsia cause no problems and improve soon after the baby is delivered, there\\'s a risk of serious complications that can affect both the mother and her baby.\\nThere\\'s a risk that the mother will develop fits called \"eclampsia\". These fits can be life threatening for the mother and baby, but they\\'re rare.\\nPage last reviewed: 28 September 2021\\nNext review due: 28 September 2024\\nNext\\n:\\nSymptoms\\nSupport links\\nHome\\nHealth A to Z\\nLive Well\\nMental health\\nCare and support\\nPregnancy\\nNHS services\\nCoronavirus (COVID-19)\\nNHS App\\nFind my NHS number\\nYour health records\\nAbout the NHS\\nHealthcare abroad\\nContact us\\nOther NHS websites\\nProfile editor login\\nAbout us\\nAccessibility statement\\nOur policies\\nCookies\\n© Crown copyright'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nhs_text[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"Cookies on the NHS website\\nWe've put some small files called cookies on your device to make our site work.\\nWe'd also like to use analytics cookies. These send information about how our site is used to services called Adobe Analytics, Hotjar and Google Analytics. We use this information to improve our site.\\nLet us know if this is OK. We'll use a cookie to save your choice. You can read more about our cookies before you choose.\\nI'm OK with analytics cookies Do not use analytics cookies\\nSearch the NHS website\\nSearch\\nMy account\\nHealth A-Z\\nLive Well\\nMental health\\nCare and support\\nPregnancy\\nBrowse\\nMore\\nHome Health A to Z\\nOverview\\n-\\nAcute lymphoblastic leukaemia\\nContents\\nOverview\\nDiagnosis\\nTreatment\\nComplications\\nAcute lymphoblastic leukaemia is a type of cancer that affects white blood cells. It progresses quickly and aggressively and requires immediate treatment. Both adults and children can be affected.\\nAcute lymphoblastic leukaemia is rare, with around 790 people diagnosed with the condition each year in the UK. Most cases of acute lymphoblastic leukaemia develop in children, teenagers and young adults.\\nAlthough it is rare, acute lymphoblastic leukaemia is the most common type of leukaemia that affects children. About 85% of the cases that affect children happen in those younger than 15 (mostly between the ages of 0 and 5). It affects slightly more boys than girls.\\nAcute lymphoblastic leukaemia is different to other types of leukaemia, including acute myeloid leukaemia, chronic lymphocytic leukaemia and chronic myeloid leukaemia.\\nInformation:\\nCoronavirus advice\\nGet advice about coronavirus and cancer:\\nMacmillan: Coronavirus guidance for people with cancer\\nCancer Research UK: Coronavirus and cancer\\nWhat happens in acute lymphoblastic leukaemia\\nAll the blood cells in the body are produced by bone marrow, which is a spongy material found inside bones.\\nBone marrow produces stem cells, which have the ability to develop into three important types of blood cells:\\nred blood cells – which carry oxygen around the body\\nwhite blood cells – which help fight infection\\nplatelets – which help stop bleeding\\nBone marrow does not usually release stem cells into the blood until they have become fully developed blood cells. But in acute lymphoblastic leukaemia, large numbers of white blood cells are released before they are ready. These are known as blast cells.\\nAs the number of blast cells increases, the number of red blood cells and platelet cells decreases. This causes the symptoms of anaemia, such as tiredness, breathlessness and an increased risk of excessive bleeding.\\nAlso, blast cells are less effective than mature white blood cells at fighting bacteria and viruses, making you more vulnerable to infection.\\nSymptoms of acute lymphoblastic leukaemia\\nAcute lymphoblastic leukaemia usually starts slowly before rapidly becoming severe as the number of immature white blood cells (blast cells) in your blood increases.\\nMost of the symptoms are caused by a lack of healthy blood cells. Symptoms include:\\npale skin\\nfeeling tired and breathless\\nrepeated infections over a short time\\nunusual and frequent bleeding, such as bleeding gums or nosebleeds\\nhigh temperature\\nnight sweats\\nbone and joint pain\\neasily bruised skin\\nswollen lymph nodes (glands)\\ntummy (abdominal pain) – caused by a swollen liver or spleen\\nunintentional weight loss\\na purple skin rash (purpura)\\nIn some cases, the affected cells can spread from your bloodstream into your central nervous system. This can cause neurological symptoms (related to the brain and nervous system), including:\\nheadaches\\nseizures or fits\\nbeing sick\\nblurred vision\\ndizziness\\nWhen to get medical advice\\nIf you or your child has some or all the symptoms listed on this page, it's still highly unlikely that acute leukaemia is the cause. However, see a GP as soon as possible because any condition that causes these symptoms needs prompt investigation and treatment.\\nFind out more about diagnosing acute lymphoblastic leukaemia.\\nWhat causes acute lymphoblastic leukaemia\\nA genetic change (mutation) in the stem cells causes immature white blood cells to be released into the bloodstream.\\nWhat causes the DNA mutation to happen is not yet understood, but known risk factors include:\\nprevious chemotherapy – if you've had chemotherapy to treat another type of cancer in the past, your risk of developing acute lymphoblastic leukaemia is increased. The risk relates to certain types of chemotherapy medicine, such as etoposide, and how much treatment you had\\nsmoking – smokers are much more likely to develop acute leukaemia than non-smokers, and studies have shown that parents who smoke in the home may increase the risk of leukaemia in their children\\nbeing very overweight (obese) – some studies have shown that people who are very overweight have a slightly higher risk of developing leukaemia than those who are a healthy weight\\ngenetic disorders – a small number of cases of childhood acute lymphoblastic leukaemia are thought to be related to genetic disorders, including Down's syndrome\\nhaving a weakened immune system – people with lowered immunity (as a result of having HIV or AIDS or taking immunosuppressants) have an increased risk of developing leukaemia\\nEnvironmental factors\\nExtensive research has been done to determine whether the following environmental factors could be a trigger for leukaemia:\\nliving near a nuclear power station\\nliving near a power line\\nliving near a building or facility that releases electro-magnetic radiation, such as a mobile phone mast\\nThere's currently no firm evidence to suggest that any of these environmental factors increases the risk of developing leukaemia.\\nCancer Research UK has more information about acute lymphoblastic leukaemia risks and causes.\\nTreating acute lymphoblastic leukaemia\\nAs acute lymphoblastic leukaemia is an aggressive condition that develops quickly, treatment usually begins a few days after diagnosis.\\nTreatment is usually done in the following stages: \\nremission induction – the first stage of treatment aims to kill the leukaemia cells in your bone marrow, restore the balance of cells in your blood and resolve any symptoms you may have\\nconsolidation – this stage aims to kill any remaining leukaemia\\nmaintenance – this stage involves taking regular doses of chemotherapy medicines to prevent leukaemia from returning\\nChemotherapy is the main treatment for acute lymphoblastic leukaemia. Other treatments you may need include antibiotics and blood transfusions. Sometimes a stem cell transplant may also be needed to achieve a cure.\\nFind out more about treating acute lymphoblastic leukaemia.\\nComplications of acute lymphoblastic leukaemia\\nIf a cure for acute lymphoblastic leukaemia is not possible, there's a risk that the lack of healthy blood cells can make the person:\\nextremely vulnerable to life-threatening infections (because they do not have enough healthy white blood cells to fight infections)\\nprone to uncontrolled and serious bleeding (because there are not enough platelets in their blood)\\nThese two complications, and others, are discussed further in complications of acute lymphoblastic leukaemia.\\nOutlook\\nOne of the biggest factors that affects the outlook for people with acute lymphoblastic leukaemia is age. The younger a person is when they are diagnosed and treatment begins, the better the outlook.\\nFrom the available data in England it is estimated that:\\nin those aged 14 or younger, more than 9 in 10 will survive leukaemia for 5 years or longer after diagnosis\\nin those aged 15 to 24, almost 7 in 10 will survive leukaemia for 5 years or longer after diagnosis\\nin those aged 25 to 64, almost 4 in 10 will survive leukaemia for 5 years or longer after diagnosis\\nin those aged 65 or older, almost 15 in 100 will survive leukaemia for 5 years or longer after diagnosis\\nHelp and support\\nFind more information about cancer.\\nIf you or a family member has been diagnosed with acute lymphoblastic leukaemia, Leukaemia Care provides further information, advice and support.\\nCall Leukaemia Care's free helpline on 08088 010 444 or email: support@leukaemiacare.org.uk\\nThe charity Cancer UK also has more information about acute lymphoblastic leukaemia.\\nPage last reviewed: 30 September 2019\\nNext review due: 30 September 2022\\nNext\\n:\\nDiagnosis\\nSupport links\\nHome\\nHealth A to Z\\nLive Well\\nMental health\\nCare and support\\nPregnancy\\nNHS services\\nCoronavirus (COVID-19)\\nNHS App\\nFind my NHS number\\nYour health records\\nAbout the NHS\\nHealthcare abroad\\nContact us\\nOther NHS websites\\nProfile editor login\\nAbout us\\nAccessibility statement\\nOur policies\\nCookies\\n© Crown copyright\""
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nhs_text[1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Clearly there is some data cleanup required to remove the generic text found on each page."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"Cookies on the NHS website\\nWe've put some small files called cookies on your device to make our site work.\\nWe'd also like to use analytics cookies. These send information about how our site is used to services called Adobe Analytics, Hotjar and Google Analytics. We use this information to improve our site.\\nLet us know if this is OK. We'll use a cookie to save your choice. You can read more about our cookies before you choose.\\nI'm OK with analytics cookies Do not use analytics cookies\\nSearch the NHS website\\nSearch\\nMy account\\nHealth A-Z\\nLive Well\\nMental health\\nCare and support\\nPregnancy\\nBrowse\\nMore\\nHome Health A to Z\\n\""
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nhs_text[0][:623]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"Cookies on the NHS website\\nWe've put some small files called cookies on your device to make our site work.\\nWe'd also like to use analytics cookies. These send information about how our site is used to services called Adobe Analytics, Hotjar and Google Analytics. We use this information to improve our site.\\nLet us know if this is OK. We'll use a cookie to save your choice. You can read more about our cookies before you choose.\\nI'm OK with analytics cookies Do not use analytics cookies\\nSearch the NHS website\\nSearch\\nHealth A-Z\\nLive Well\\nMental health\\nCare and support\\nPregnancy\\nBrowse\\nMore\\nHome Health A to Z\\nHomeopathy\\n\""
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nhs_text[2][:623]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"Cookies on the NHS website\\nWe've put some small files called cookies on your device to make our site work.\\nWe'd also like to use analytics cookies. These send information about how our site is used to services called Adobe Analytics, Hotjar and Google Analytics. We use this information to improve our site.\\nLet us know if this is OK. We'll use a cookie to save your choice. You can read more about our cookies before you choose.\\nI'm OK with analytics cookies Do not use analytics cookies\\nSearch the NHS website\\nSearch\\nMy account\\nHealth A-Z\\nLive Well\\nMental health\\nCare and support\\nPregnancy\\nBrowse\\nMore\\nHome Health A to Z\\n\""
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nhs_text[5][:623]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "import re\n",
    "\n",
    "header = re.compile(r'(?s)Cookies.*\\nHome Health A to Z\\n')\n",
    "\n",
    "def clean(text):\n",
    "    text = header.sub('', text)\n",
    "    text = re.sub(r'\\n+', '\\n', text)\n",
    "    text = text.split(\"Page last reviewed:\")[0]\n",
    "    return text"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Overview\\n-\\nPre-eclampsia\\nContents\\nOverview\\nSymptoms\\nCauses\\nDiagnosis\\nTreatment\\nComplications\\nPre-eclampsia is a condition that affects some pregnant women, usually during the second half of pregnancy (from 20 weeks) or soon after their baby is delivered.\\nImportant:\\nCoronavirus (COVID-19) update\\nIf you\\'re well, it\\'s really important you go to all your appointments and scans for the health of you and your baby.\\nIf you\\'re pregnant, hospitals and clinics are making sure it\\'s safe for you to go to appointments.\\nIf you get symptoms of COVID-19, or you\\'re unwell with something other than COVID-19, speak to your midwife or maternity team. They will advise you what to do.\\nFind out more about pregnancy and COVID-19\\nSymptoms of pre-eclampsia\\nEarly signs of pre-eclampsia include having high blood pressure (hypertension) and protein in your urine (proteinuria). \\nIt\\'s unlikely that you\\'ll notice these signs, but they should be picked up during your routine antenatal appointments.\\nIn some cases, further symptoms can develop, including:\\nsevere headache\\nvision problems, such as blurring or flashing\\npain just below the ribs\\nvomiting\\nsudden swelling of the face, hands or feet\\nIf you notice any symptoms of pre-eclampsia, seek medical advice immediately by calling your midwife, GP surgery or NHS 111.\\nAlthough many cases are mild, the condition can lead to serious complications for both mother and baby if it\\'s not monitored and treated. \\nThe earlier pre-eclampsia is diagnosed and monitored, the better the outlook for mother and baby.\\nVideo: what is pre-eclampsia and what are the warning signs?\\nIn this video, a midwife explains the warning signs of pre-eclampsia.\\nPlay Video\\nMedia last reviewed: 1 September 2020\\nMedia review due: 1 September 2023\\nWho\\'s affected?\\nThere are a number of things that can increase your chances of developing pre-eclampsia, such as:\\nhaving diabetes, high blood pressure or kidney disease before you were pregnant\\nhaving an autoimmune condition, such as lupus or antiphospholipid syndrome\\nhaving high blood pressure or pre-eclampsia in a previous pregnancy\\nOther things that can slightly increase your chances of developing pre-eclampsia include:\\na family history of pre-eclampsia\\nbeing 40 years old or more\\nit\\'s more than 10 years since your last pregnancy\\nexpecting multiple babies (twins or triplets)\\nhaving a body mass index (BMI) of 35 or more\\nIf you have 2 or more of these together, your chances are higher.\\nIf you\\'re thought to be at a high risk of developing pre-eclampsia, you may be advised to take a 75 to 150mg daily dose of aspirin from the 12th week of pregnancy until your baby is born.\\nWhat causes pre-eclampsia?\\nAlthough the exact cause of pre-eclampsia is not known, it\\'s thought to occur when there\\'s a problem with the placenta, the organ that links the baby\\'s blood supply to the mother\\'s.\\nTreating pre-eclampsia\\nIf you\\'re diagnosed with pre-eclampsia, you should be referred for an assessment by a specialist, usually in hospital.\\nWhile in hospital, you\\'ll be monitored closely to determine how severe the condition is and whether a hospital stay is needed.\\nThe only way to cure pre-eclampsia is to deliver the baby, so you\\'ll usually be monitored regularly until it\\'s possible for your baby to be delivered.\\nThis will normally be at around 37 to 38 weeks of pregnancy, but it may be earlier in more severe cases.\\nAt this point, labour may be started artificially (induced) or you may have a caesarean section.\\nYou\\'ll be offered medicine to lower your blood pressure while you wait for your baby to be delivered.\\nComplications\\nAlthough most cases of pre-eclampsia cause no problems and improve soon after the baby is delivered, there\\'s a risk of serious complications that can affect both the mother and her baby.\\nThere\\'s a risk that the mother will develop fits called \"eclampsia\". These fits can be life threatening for the mother and baby, but they\\'re rare.\\n'"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "clean(nhs_text[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"Glue ear\\nGlue ear is where the empty middle part of the ear canal fills up with fluid. This can cause temporary hearing loss. It usually clears up within 3 months, but see a GP about any hearing problems.\\nCheck if it's glue ear\\nThe most common symptom of glue ear is temporary hearing loss. It can affect both ears at the same time.\\nOther symptoms may include:\\nearache or ear pain\\nhearing sounds like ringing or buzzing (tinnitus)\\nGlue ear is much more common in children, but adults with glue ear have the same symptoms.\\nOther conditions that cause ear pain\\nNon-urgent advice:\\nSee a GP if your child has hearing problems\\nYour child may be struggling to hear if they often:\\nspeak loudly\\nare difficult to understand\\nask people to repeat what they say\\nask for the TV or music to be turned up loud\\nstruggle to hear people far away\\nbecome easily distracted when people are talking\\nseem tired and irritable because it's harder to listen\\nInformation:\\nCoronavirus (COVID-19) update: how to contact a GP\\nIt's still important to get help from a GP if you need it. To contact your GP surgery:\\nvisit their website\\nuse the NHS App\\ncall them\\nFind out about using the NHS during COVID-19\\nWhat happens at your appointment\\nThe GP should be able to tell if it's glue ear by looking for fluid inside the ear.\\nThey'll use a small scope with a light and magnifying glass. This should not be painful.\\nIf your child has had glue ear for more than 3 months, they may be referred to a specialist for hearing tests.\\nHearing tests can help find out how severe any hearing loss is and what's causing it.\\nTreatment for glue ear from a GP\\nGlue ear is not always treated. The GP will usually wait to see if the symptoms get better on their own.\\nThis is because there's no effective medicine for glue ear, and it often clears up on its own within 3 months.\\nYour child may be monitored for up to a year in case their symptoms change or get worse.\\nThe GP may suggest trying a treatment called autoinflation while waiting for symptoms to improve. Autoinflation can help fluid in the ear to drain.\\nIt's done by either:\\nblowing up a special balloon using 1 nostril at a time\\nswallowing while holding the nostrils closed\\nAs autoinflation has to be done several times a day, it's not usually recommended for children under 3 years old.\\nAntibiotics may be prescribed if glue ear causes an ear infection.\\nHospital treatment for glue ear\\nYour child may be referred to a specialist in hospital if:\\nglue ear symptoms are affecting their learning and development\\nthey already had severe hearing loss before glue ear\\nthey have Down's syndrome or a cleft lip and palate, as glue ear is less likely to get better by itself\\nThe 2 main treatments are temporary hearing aids or grommets (small tubes implanted in the ear).\\nOccasionally, surgery may be recommended to remove some glands at the back of the nose (adenoids). This is known as an adenoidectomy.\\nThe specialist in hospital will help you decide on the best treatment option.\\nGrommets for treating glue ear\\nA grommet is a small tube that's placed in your child's ear during surgery. It drains fluid away and keeps the eardrum open.\\nThe grommet should fall out naturally within 6 to 12 months as your child's ear gets better.\\nIf your child needs grommets, you might find these links useful:\\nGreat Ormond Street Hospital (GOSH): treatment of glue ear with grommets\\nNational Deaf Children's Society (NDCS): Harvey gets grommets\\nVideo: What is glue ear?\\nThis animation explains in detail what glue ear is, what causes it and how it's treated.\\nPlay Video\\nMedia last reviewed: 1 April 2021\\nMedia review due: 1 April 2024\\n\""
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "clean(nhs_text[100])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This cleaning function seems to work well enough so we can apply it to our data to returning a cleaner set of results."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "nhs_text = [clean(text) for text in nhs_text]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Our embedding model expects no more than 128 *tokens* of text, this translates to roughly 400-600 characters, so we will split the text into chunks of ~500 characters with a few extra conditions:\n",
    "\n",
    "* We split on newline characters `\\n`\n",
    "* We leave an overlap of one sentence between each chunk (to avoid missing relevant relationships between sentences)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "chunked = []\n",
    "chunk = 500\n",
    "\n",
    "for i, page in enumerate(nhs_text):\n",
    "    url = paths[i][8:-5].replace('_', '/')\n",
    "    page = page.split(\"\\n\")\n",
    "    context = \"\"\n",
    "    for j in range(len(page)):\n",
    "        if j != 0 and len(context) == 0:\n",
    "            context += page[j-1] + \" \"\n",
    "        context += page[j] + \" \"\n",
    "        if len(context) >= chunk:\n",
    "            chunked.append({\n",
    "                \"text\": context,\n",
    "                \"url\": url\n",
    "            })\n",
    "            context = \"\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "*If you'd like to keep things simpler, we can avoid adding the sentence overlap and cutting on newline characters with:*\n",
    "\n",
    "```python\n",
    "chunked = []\n",
    "chunk = 500\n",
    "\n",
    "for i, page in enumerate(nhs_text):\n",
    "    url = paths[i][8:]\n",
    "    for i in range(0, len(page), chunk):\n",
    "        i_end = min(i + chunk, len(page))\n",
    "        chunked.append({\n",
    "            \"text\": page[i:i_end],\n",
    "            \"url\": url\n",
    "        })\n",
    "```\n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'text': \"Overview - Pre-eclampsia Contents Overview Symptoms Causes Diagnosis Treatment Complications Pre-eclampsia is a condition that affects some pregnant women, usually during the second half of pregnancy (from 20 weeks) or soon after their baby is delivered. Important: Coronavirus (COVID-19) update If you're well, it's really important you go to all your appointments and scans for the health of you and your baby. If you're pregnant, hospitals and clinics are making sure it's safe for you to go to appointments. \",\n",
       " 'url': 'www.nhs.uk/conditions/pre-eclampsia'}"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chunked[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'text': \"If you're pregnant, hospitals and clinics are making sure it's safe for you to go to appointments. If you get symptoms of COVID-19, or you're unwell with something other than COVID-19, speak to your midwife or maternity team. They will advise you what to do. Find out more about pregnancy and COVID-19 Symptoms of pre-eclampsia Early signs of pre-eclampsia include having high blood pressure (hypertension) and protein in your urine (proteinuria).  It's unlikely that you'll notice these signs, but they should be picked up during your routine antenatal appointments. \",\n",
       " 'url': 'www.nhs.uk/conditions/pre-eclampsia'}"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chunked[1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we can see the sentence overlap `\"If you're pregnant, hospitals and clinics are making sure it's safe for you to go to appointments.\"` shared between the two chunks. We also split chunks between sentences rather than mid-word (which would be the case if cutting on every 500 characters without consideration of newlines)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Indexing the Data\n",
    "\n",
    "With our data prepared we can begin indexing it. First, we initialize the document store."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`!pip install -U 'farm-haystack[pinecone]'`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO - haystack.modeling.model.optimization -  apex not found, won't use it. See https://nvidia.github.io/apex/\n",
      "ERROR - root -  Failed to import 'magic' (from 'python-magic' and 'python-magic-bin' on Windows). FileTypeClassifier will not perform mimetype detection on extensionless files. Please make sure the necessary OS libraries are installed if you need this functionality.\n",
      "INFO - haystack.document_stores.pinecone -  Index statistics: name: haystack-nhs-jul, embedding dimensions: 768, record count: 0\n"
     ]
    }
   ],
   "source": [
    "from haystack.document_stores import PineconeDocumentStore\n",
    "\n",
    "API_KEY = \"<<YOUR_API_KEY>>\"\n",
    "INDEX_NAME = \"haystack-nhs-jul\"\n",
    "\n",
    "document_store = PineconeDocumentStore(\n",
    "    api_key=API_KEY,\n",
    "    index=INDEX_NAME,\n",
    "    similarity=\"dot_product\",\n",
    "    embedding_dim=768,\n",
    "    metadata_config={\"indexed\": [\"url\"]}\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And now we create our documents and add them to the document store."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
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     "metadata": {},
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    },
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     "data": {
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     },
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    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "9cf5910bba05451eb2fcf52d161b127e",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "7f983964d3634a10a218c9535f05ebd2",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Writing Documents:   0%|          | 0/256 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "5774b0be1900414695343cf034839381",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
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      ]
     },
     "metadata": {},
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    }
   ],
   "source": [
    "from haystack import Document\n",
    "from tqdm.auto import tqdm  # progress bar\n",
    "\n",
    "batch_size = 256\n",
    "\n",
    "counter = 0\n",
    "docs = []\n",
    "\n",
    "for d in tqdm(chunked):\n",
    "    # create haystack document object with text content and doc metadata\n",
    "    doc = Document(\n",
    "        content=d[\"text\"],\n",
    "        meta={\n",
    "            \"url\": d[\"url\"]\n",
    "        }\n",
    "    )\n",
    "    docs.append(doc)\n",
    "    counter += 1\n",
    "    if counter % batch_size == 0:\n",
    "        # writing docs everytime 10k docs are reached\n",
    "        document_store.write_documents(docs)\n",
    "        docs.clear()\n",
    "\n",
    "if len(docs) > 0:\n",
    "    document_store.write_documents(docs)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Although we have added the documents to our document store, they do not include *embeddings*, which are required for us to perform a vector search. To create these embeddings we need to initialize a retriever model."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO - haystack.modeling.utils -  Using devices: CPU\n",
      "INFO - haystack.modeling.utils -  Number of GPUs: 0\n",
      "INFO - haystack.retriever.dense -  Init retriever using embeddings of model sentence-transformers/multi-qa-mpnet-base-dot-v1\n",
      "WARNING - haystack.nodes.retriever._embedding_encoder -  You are using a Sentence Transformer with the dot_product function. We recommend using cosine instead. This can be set when initializing the DocumentStore\n"
     ]
    }
   ],
   "source": [
    "from haystack.nodes import EmbeddingRetriever\n",
    "\n",
    "retriever = EmbeddingRetriever(\n",
    "    document_store=document_store,\n",
    "    embedding_model='sentence-transformers/multi-qa-mpnet-base-dot-v1',\n",
    "    model_format=\"sentence_transformers\"\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
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     "text": [
      "INFO - haystack.document_stores.pinecone -  Updating embeddings for 8521 docs...\n"
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   ],
   "source": [
    "document_store.update_embeddings(\n",
    "    retriever,\n",
    "    batch_size=16\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can check that our documents have been added using a simple `DocumentSearchPipeline`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
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    {
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     "output_type": "stream",
     "text": [
      "\n",
      "Query: Who is affected by pre-eclampsia?\n",
      "\n",
      "{   'content': 'Overview - Pre-eclampsia Contents Overview Symptoms Causes '\n",
      "               'Diagnosis Treatment Complications Pre-eclampsia is a condition '\n",
      "               'that affects some pregnant women, usually during the second '\n",
      "               'half of pregnancy (from 20 weeks) or soon after their baby is '\n",
      "               \"delivered. Important: Coronavirus (COVID-19) update If you're \"\n",
      "               \"well, it's really important you go to all your appointments \"\n",
      "               \"and scans for the health of you and your baby. If you're \"\n",
      "               \"pregnant, hospitals and clinics are making sure it's safe for \"\n",
      "               'you to go to appointments. ',\n",
      "    'name': None}\n",
      "\n",
      "{   'content': 'Although many cases are mild, the condition can lead to '\n",
      "               \"serious complications for both mother and baby if it's not \"\n",
      "               'monitored and treated.  The earlier pre-eclampsia is diagnosed '\n",
      "               'and monitored, the better the outlook for mother and baby. '\n",
      "               'Video: what is pre-eclampsia and what are the warning signs? '\n",
      "               'In this video, a midwife explains the warning signs of '\n",
      "               'pre-eclampsia. Play Video Media last reviewed: 1 September '\n",
      "               \"2020 Media review due: 1 September 2023 Who's affected? There \"\n",
      "               'are a number of things that can increase your chances of '\n",
      "               'developing pre-eclampsia, such as: ',\n",
      "    'name': None}\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from haystack.pipelines import DocumentSearchPipeline\n",
    "from haystack.utils import print_documents\n",
    "\n",
    "search_pipe = DocumentSearchPipeline(retriever)\n",
    "result = search_pipe.run(\n",
    "    query=\"Who is affected by pre-eclampsia?\",\n",
    "    params={\"Retriever\": {\"top_k\": 2}}\n",
    ")\n",
    "\n",
    "print_documents(result)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This all looks good and we're returning relevant information for our query.\n",
    "\n",
    "This is just the indexing step, eg adding the data/documents + their embeddings to our document store. In the following notebook *01_test_pipeline.ipynb* we will initialize and test a full *extractive QA* pipeline.\n",
    "\n",
    "---"
   ]
  }
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